rs1931992

Variant names:

• chr6-142280070-A-C
• rs1931992
• ENST00000849528.1:n.102-10787T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000849528.1(ENSG00000310391):​n.102-10787T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 151,908 control chromosomes in the GnomAD database, including 11,317 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.38 (11317 hom., cov: 30)
• Consequence: ENSG00000310391 ENST00000849528.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 4 publications found

Genes affected

ENSG00000310391 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310391	ENST00000849528.1	n.102-10787T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57313 AN: 151788 Hom.: 11320 Cov.: 30

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.399

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.377 AC: 57333 AN: 151908 Hom.: 11317 Cov.: 30 AF XY: 0.376 AC XY: 27956 AN XY: 74254

African (AFR) AF: 0.271 AC: 11214 AN: 41428

American (AMR) AF: 0.389 AC: 5932 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1572 AN: 3468

East Asian (EAS) AF: 0.199 AC: 1023 AN: 5142

South Asian (SAS) AF: 0.433 AC: 2083 AN: 4814

European-Finnish (FIN) AF: 0.408 AC: 4313 AN: 10560

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.438 AC: 29779 AN: 67918

Other (OTH) AF: 0.397 AC: 837 AN: 2108

Alfa AF: 0.400 Hom.: 1651

Bravo AF: 0.367

Asia WGS AF: 0.336 AC: 1167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.23
DANN	Benign	0.36
PhyloP100		-1.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1931992; hg19: chr6-142601207;